Device and method for thermal cycling

ABSTRACT

A thermal cycling device for performing nucleic acid amplification on a plurality of biological samples positioned in a sample well tray. The thermal cycling device includes a sample block assembly, an optical detection system, and a sample well tray holder configured to hold the sample well tray. The sample block assembly is adapted for movement between a first position permitting the translation of the sample well tray into alignment with sample block assembly, and a second position, upward relative to the first position, where the sample block assembly contacts the sample well tray. A method of performing nucleic acid amplification on a plurality of biological samples positioned in a sample well tray in a thermal cycling device is also provided.

[0001] The present invention relates generally to a thermal cyclingdevice and method of performing nucleic acid amplification on aplurality of biological samples positioned in a sample well tray. Moreparticularly, the present invention relates in one aspect to a thermalcycling device and method of real-time detection of a nucleic acidamplification process such as polymerase chain reaction (PCR).

BACKGROUND

[0002] Biological testing has become an important tool in detecting andmonitoring diseases. In the biological testing field, thermal cycling isused to amplify nucleic acids by, for example, performing PCR and otherreactions. PCR in particular has become a valuable research tool withapplications such as cloning, analysis of genetic expression, DNAsequencing, and drug discovery.

[0003] Recent developments in the field have spurred growth in thenumber of tests that are performed. One method for increasing thethroughput of such biological testing is to provide real-time detectioncapability during thermal cycling. Real-time detection increases theefficiency of the biological testing because the characteristics of thesamples can be detected while the sample well tray remains positioned inthe thermal cycling device, therefore not requiring removal of thesample well tray to a separate area prior to testing of the samples. Intypical real-time thermal cycling devices, the sample well tray isremoved after detection is completed.

SUMMARY OF THE INVENTION

[0004] Various aspects of the invention generally relate to a thermalcycling device in which the sample block assembly may be verticallymoved so that the sample well tray may be inserted and removed from thethermal cycling device. The thermal cycling device can be a real-timedevice. During such movement of the sample block assembly and samplewell tray, the optical detection system can remain substantiallystationary.

[0005] According to one aspect, the invention comprises a thermalcycling device. The thermal cycling device includes a sample blockassembly, an optical detection system, and a sample well tray holder.The sample well tray holder includes a tray-receiving region configuredto hold a sample well tray. The optical detection system is positionedabove the sample block assembly. The sample well tray holder isconfigured to translate the sample well tray into alignment with thesample block assembly. The sample block assembly is adapted for movementbetween a first position permitting the translation of the sample welltray into alignment with the sample block assembly, and a secondposition, upward relative to the first position, where the sample blockassembly contacts the sample well tray.

[0006] In another aspect, the optical detection system is adapted toremain substantially stationary during insertion and removal of thesample well tray from the thermal cycling device. In a further aspect,the thermal cycling device further includes a positioning mechanismconfigured to translate the sample block between the first and secondpositions.

[0007] In yet another aspect, the invention comprises a method ofperforming nucleic acid amplification on a plurality of biologicalsamples positioned in a sample well tray in a thermal cycling device.The method includes the step of placing the sample well tray into asample well tray holder. The method further includes the step oftranslating the sample well tray holder and sample well tray into thethermal cycling device until the sample well tray is aligned with asample block assembly positioned beneath the sample well tray. Themethod further includes the step of translating the sample blockassembly from a first position to a second position. In the firstposition, the sample block assembly permits the sample well tray totranslate into alignment with the sample block assembly. In the secondposition, the sample block assembly is positioned vertically upwardrelative to the first position to contact the sample well tray.

[0008] The method can further comprise the step of thermally cycling thedevice while simultaneously optically detecting the samples. The methodcan further comprise translating the sample block assembly from thesecond position to the first position. Finally, the method can comprisethe step of removing the sample well tray holder and sample well trayfrom the thermal cycling device. In various embodiments, the opticaldetection system remains substantially stationary throughout the abovesteps.

[0009] In another aspect, the invention comprises a thermal cyclingdevice. The thermal cycling device includes an optical detection system,a sample block, and a sample well tray holder. The sample block isadapted for movement along a first path, toward and away from theoptical detection system. The sample well tray holder includes atray-receiving region. The sample well tray holder is adapted formovement along a second path, toward and away from a position whereatthe tray-receiving region is disposed between the optical detectionsystem and the sample block. The optical detection system can be adaptedto remain substantially stationary during movement of the sample blockand the sample well tray holder along the first and second paths.

[0010] It is to be understood that both the foregoing generaldescription and the following detailed description are exemplary andexplanatory only and are not restrictive of the invention, as claimed.

BRIEF DESCRIPTION OF THE DRAWINGS

[0011] The accompanying drawings, which are incorporated in andconstitute a part of this specification, illustrate several embodimentsof the invention. In the drawings,

[0012]FIG. 1 is a front view of an exemplary embodiment of a thermalcycling device according to the present invention;

[0013]FIG. 2A is side view of an embodiment of the device of FIG. 1,with a sample well tray positioned outside of the device;

[0014]FIG. 2B is a side view of the device of FIG. 1, with the samplewell tray inserted into the device;

[0015]FIG. 2C is a side view of the device of FIG. 1, with the samplewell tray inserted into the device and a sample block assembly in anupward position for engaging the sample well tray;

[0016]FIG. 3A is a side view of another embodiment of the thermalcycling device of the invention, with a sample well tray positionedoutside of the device;

[0017]FIG. 3B is a side view of the device of FIG. 3A, with the samplewell tray inserted into the device;

[0018]FIG. 3C is a side view of the device of FIG. 3A, with the samplewell tray inserted into the device and a sample block assembly in anupward position for engaging the sample well tray;

[0019]FIG. 4A is side view of yet another embodiment of the thermalcycling device of the invention, with the sample well tray positionedoutside of the device;

[0020]FIG. 4B is a side view of the device of FIG. 4A, with the samplewell tray inserted into the device;

[0021]FIG. 4C is a side view of the device of FIG. 4A, with the samplewell tray inserted into the device and a sample block assembly in anupward position for engaging the sample well tray;

[0022]FIG. 5 is a side cross sectional view of a sample well trayholder, used with the present invention, with a sample well traypositioned thereon; and

[0023]FIG. 6 is a perspective view of one embodiment of a sample blockassembly used in the device of the invention.

DESCRIPTION OF CERTAIN EMBODIMENTS

[0024] Reference will now be made to certain exemplary embodiments ofthe invention, examples of which are illustrated in the accompanyingdrawings. Wherever possible, the same reference numbers are used in thedrawings and the description to the same or like parts.

[0025] In accordance with certain embodiments, a thermal cycling deviceis provided. In one aspect, the thermal cycling device may performnucleic acid amplification on a plurality of biological samplespositioned in a sample well tray. In certain embodiments, the thermalcycling device includes a sample block assembly, an optical detectionsystem positioned above the sample block assembly, and a sample welltray holder with a tray-receiving region configured to hold the samplewell tray. In certain aspects, the sample block assembly is adapted formovement between a first position permitting the translation of thesample well tray into alignment with the sample block assembly, and asecond position, upward relative to the first position, where the sampleblock assembly contacts the sample well tray. The thermal cycling devicemay also include a positioning mechanism for translating the sampleblock between the first and second positions.

[0026] Although the terms “horizontal,” “vertical,” “upward,” and“downward” are used in describing various aspects of the presentinvention, it should be understood that such terms are for purposes moreeasily describing the invention, and do not limit the scope of theinvention.

[0027] In various embodiments, such as illustrated in FIGS. 1, 2A-2C,and 5-6, the thermal cycling device 10 for performing nucleic acidamplification on a plurality of biological samples includes one or moreof: a sample block assembly 50; an optical detection system 12 fordetecting the characteristics of the samples positioned in a sample welltray 14; a sample well tray holder 30; and a positioning mechanism 70connected to the sample block assembly, the positioning mechanism beingconfigured to impart vertical movement on the sample block assembly.

[0028] The thermal cycling device is typically configured to performnucleic acid amplification. One common method of performing nucleic acidamplification of biological samples is polymerase chain reaction (PCR).Various PCR methods are known in the art, as described in, for example,U.S. Pat. Nos. 5,928,907 and 6,015,674 to Woudenberg et al., thecomplete disclosures of which are hereby incorporated by reference forany purpose. Other methods of nucleic acid amplification include, forexample, ligase chain reaction, oligonucleotide litigations assay, andhybridization assay. These and other methods are described in greaterdetail in U.S. Pat. Nos. 5,928,907 and 6,015,674.

[0029] In one embodiment, the thermal cycling device performs real-timedetection of the nucleic acid amplification of the samples duringthermal cycling. Real-time detection systems are known in the art, asalso described in greater detail in, for example, U.S. Pat. Nos.5,928,907 and 6,015,674 to Woudenberg et al., incorporated herein above.During real-time detection, various characteristics of the samples aredetected during the thermal cycling in a manner known in the art.Real-time detection permits more accurate and efficient detection andmonitoring of the samples during the nucleic acid amplification.

[0030] In accordance with various embodiments, the thermal cyclingdevice includes an optical detection system. As embodied herein andshown in FIGS. 1 and 2A-2C, an optical detection system 12 is positionedabove the sample block assembly 50. The optical detection system 12 isconfigured to detect and monitor the characteristics of the samples inthe sample well tray 14 in real-time during the thermal cycling.Suitable structures and methods for the optical detection system 12 arewell known in the art. The optical detection system may use any knownstructure or method. In one example, the optical detection system wouldinclude a quartz bulb with a CCD camera, in a manner known in the art.In another example, the optical detection system may include afluorescence based system with a lens and a fiber optics for each cableas described in U.S. Pat. Nos. 5,928,907 and 6,015,674 to Woudenberg etal, incorporated herein above. Alternatively, the optical detectionsystem may include any known system using a single light source for eachsample well, in a manner known in the art. Likewise, the opticaldetection system may include any other type suitable for use with thethermal cycling device of the present invention.

[0031] In various embodiments, optical detection system 12 issubstantially stationarily mounted in the thermal cycling device. Theoptical detection system can be configured so that the optical detectionsystem remains substantially stationary during insertion of a samplewell tray holder and sample well tray into the thermal cycling device,during thermal cycling of the sample well tray, during removal of thesample well tray holder and sample well tray from the thermal cyclingdevice, and at all stages in between the above steps. By remainingsubstantially stationary, the optical system reduces the potential formisalignment of the optical components. For purposes of this invention,the term “substantially stationary” does not mean that the opticaldetection system is completely stationary, rather, the term includes anyvibrations or movements caused by normal operation of the thermalcycling device.

[0032] The thermal cycling device may be configured for use with anytype of sample well tray, including, for example, 96-well sample welltrays, 384-well sample trays, and microcard sample trays. The size andshape of these sample well trays are well known in the art. Examples of96-well sample well trays suitable for use in the present invention aredescribed in WO 00/25922 to Moring et al., the complete disclosure ofwhich is hereby incorporated by reference for any purpose. Examples ofsample well trays of the microcard type suitable for use in the presentinvention are described in WO 01/28684 to Frye et al., the completedisclosure of which is hereby incorporated by reference for any purpose,WO97/36681 to Woudenberg et al., the complete disclosure of which ishereby incorporated by reference for any purpose, U.S. application Ser.No. 09/897,500, filed Jul. 3, 2001, assigned to the assignee of thepresent invention, the complete disclosure of which is herebyincorporated by reference for any purpose, and U.S. application Ser. No.09/977,225, filed Oct. 16, 2001, assigned to the assignee of the presentapplication, the complete disclosure of which is hereby incorporated byreference for any purpose. Sample well trays having any number of samplewells and sample well sizes may also be used with the thermal cyclingdevice of the present invention. In the example shown in the figures,the volume of the sample wells may vary anywhere from about 0.01 μl tothousands of microliters (μl), with a volume between 10 to 500 μl beingtypical.

[0033] As embodied herein and shown in FIGS. 1, 2A-2C, and 5, the samplewell tray 14 can include a rectangular top portion 16 having a topsurface 18 and bottom surface 24. The top surface 18 defines openingsfor a plurality of sample wells 20 of any known size and shape. In theexample shown in FIGS. 1-6, the sample well tray includes ninety-sixsample wells positioned in a well-known 8×12 array. In the embodimentshown, the top portion 16 of the sample well tray is rectangular. In theembodiment shown in the figures, the sample wells are conical shaperecesses extending downwardly from the top surface 18 in a known manner.Each sample well includes a sample well bottom surface 22 for engagingwith corresponding recesses in the sample block assembly 50. It is wellunderstood that any type of sample well configuration may be used withthe present invention, including for example, a 384-well sample welltray and a microcard type sample tray.

[0034] In accordance with various embodiments, the thermal cyclingdevice can include a sample well tray holder having a tray-receivingregion configured to hold the sample well tray. The sample well trayholder can be configured to translate the sample well tray intoalignment with a sample block assembly. As described herein and shown inFIGS. 1, 2A-2C, and 5, the sample well tray holder is generallydesignated by reference number 30. The sample well tray holder isconfigured so that the sample well tray may be supported thereon,particularly during insertion of the sample well tray into the thermalcycling device, and during removal of the sample well tray from thethermal cycling device. In various embodiments, the sample well trayholder 30 is generally rectangular in shape.

[0035] With particular reference to FIG. 5, the sample well tray holder30 includes a top surface 32 and a side surface 34 that extends aroundthe periphery of the sample well tray holder. The side surface in thefront of the device is designated by reference number 36. The samplewell tray holder further includes a tray-receiving region configured tohold a sample well tray. In the embodiment shown in FIG. 5, thetray-receiving region is defined by a downwardly projecting holderstructure 38 in the top surface 32. The downwardly projecting holderstructure 38 is positioned on a first recessed portion 40 of the topsurface 32. The downwardly projecting holder structure 38 includes ahorizontally projecting annular projection 42 for engaging the topsurface of the first recessed portion 40 of the top surface 32. Thedownwardly projecting holder structure 38 further comprises a projection44 that slopes inwardly. The inside of the projection 44 defines arectangular opening or recess slightly smaller than the sample well tray16. The rectangular opening or recess is dimensioned to receive a samplewell tray. In particular, the projection 44 is dimensioned so that thebottom surface 24 of the sample well tray may rest on the top surface ofthe projection 44, as shown in FIG. 5. The projecting holder structuremay be shaped to be angled inwardly in order to ease the removal of thesample well tray from the sample well tray holder.

[0036] The sample well tray holder 30 and sample well tray 14 aredimensioned so that they are capable of passing between the opticaldetection system 12 and the sample block assembly 50 withoutinterference during insertion into and removal from the thermal cyclingdevice. The sample well tray is configured so that it can horizontallytranslate into and out of the thermal cycling device on the sample welltray holder. In order to facilitate insertion or removal of the samplewell tray holder, bearing surfaces (not shown) may be provided on thesample well tray holder and/or thermal cycling device. The sample welltray holder may be horizontally translated either manually orautomatically.

[0037] In accordance with various embodiments, the thermal cyclingdevice can include a sample block assembly configured to receive thesample well tray thereon. As described herein and shown in FIGS. 1,2A-2C, 5, and 6, a sample block assembly is generally designated byreference number 50. It is to be understood that the sample blockassembly shown in FIG. 6 is by way of example only, and the invention isnot limited to the sample block assembly shown in FIG. 6. The sampleblock assembly shown in FIG. 6 includes a sample block 58 and a heatsink 56. Sample blocks are well known in the art. Sample blocks may bemade of any suitable material, such as aluminum. The sample blockassembly typically includes at least one heating element. In oneembodiment, the at least one heating element includes a peltier heater.Methods of heating and cooling a sample block during and after thermalcycling are known in the art. The sample block 58 shown in FIG. 6includes a top surface 54 with a plurality of recess 52 on the topsurface. The recesses are arranged to correspond to the sample wells ofthe sample well tray. For example, in the embodiment shown in FIG. 6,the sample block assembly includes ninety-six recesses for engaging witha 96-well sample well tray. Alternatively, the sample block assembly canhave any number of recesses. For example, the number of recesses canequal the number of sample wells. In an embodiment with a 384-wellsample tray, the sample block assembly would typically have at least 384recesses. In an embodiment using a microcard type sample tray, thesample block need not have recesses.

[0038] Heat sink 56 may be any known type of heat sink. Additionally, aconvection unit such as a fan may be positioned adjacent the sampleblock assembly. In the embodiment shown in FIGS. 1, 2A-2C, and 5-6, theconvection unit comprises a fan 66 positioned below the sample blockassembly 50. In one embodiment, the fan 66 creates a flow of cooling airagainst the heat sink 56 in order to cool the sample block.Alternatively, the fan may be used with a heater in order to create aflow of hot air against the heat sink in order to heat the sample block.In certain embodiments, the fan is mounted so that it moves verticallywith the sample block assembly. In other embodiments, the fan may bestationarily mounted in the thermal cycling device

[0039] In accordance with various embodiments, the thermal cyclingdevice can include a positioning mechanism connected to the sample blockassembly, the positioning mechanism being configured to verticallytranslate the sample block assembly between a first or “downward”position and a second or “upward” position. The positioning mechanismcan be configured to translate the sample block assembly between thefirst position, where the sample block assembly permits the translationof the sample well tray into alignment with the sample block assembly,and the second position, upward relative to the first position, wherethe sample block assembly contacts the sample well tray.

[0040] An embodiment of the positioning mechanism is illustrated inFIGS. 1 and 2A-2C. In the embodiment shown in FIGS. 1 and 2A-2C, thepositioning mechanism is generally designated by reference number 70.The positioning mechanism is connected to the sample block assembly 50.The positioning mechanism allows insertion and removal of the samplewell tray by moving the sample block assembly in the vertical direction.FIGS. 2A and 2B show the downward or “first” position of the sampleblock assembly. In the downward position, a gap is created between thetop of the sample block assembly 50 and a bottom portion 94 of theoptical detection system of sufficient size so that the sample well trayholder and sample well tray may be inserted therebetween. In the firstposition, the sample block is “away” from the optical detection system.

[0041] In a second or “upward” position shown in FIG. 2C, the sampleblock assembly 50 is vertically upward relative to the downward or“first” position. In the upward position, the top surface 54 of thesample block 58 presses against the bottom of the sample well tray 14 sothat the recesses 52 mate with the sample well bottom surfaces 22. Invarious embodiments using a microcard, a top surface of the sample blockcan press against a bottom surface of the microcard. In the secondposition, the sample block is “toward” the optical detection system. Thesample block assembly is adapted for movement toward and away from theoptical detection system along a predetermined vertical path.

[0042] In the embodiment shown in FIGS. 1 and 2A-2C, the positioningmechanism 70 includes a plurality of links. The arrangement of linksshown in FIGS. 1 and 2A-2C is by way of example only. The plurality oflinks includes a first link 78 as shown in FIGS. 2A-2C. The first link78 is shown as being in the shape of a connecting rod, however, thefirst link may have any number of different shapes. First link 78includes a first end 80 rotatably connected to a motor 72 at a pivotpoint 74. Motor 72 can be any known type of motor that is capable ofimparting a translational or rotational force on the first link 78. Asshown in FIGS. 2A-2C, the motor causes pivot point 74 of the first end80 to revolve around a central axis 76 of the motor. The revolution ofthe first end 80 about the central axis of the motor causes the firstlink to translate.

[0043] As shown in FIGS. 2A-2C, a second end 82 of the first link isrotatably connected to a first end of a second link 84 at pivot point88. The second link has a second end rotatably connected to stationarypivot point 86. The second link 84 pivots about stationary pivot point86 when the motor causes movement of the first link 78.

[0044] The second end 82 of the first link is rotatably connected to afirst end of a third link 90 at pivot point 88. The second end of thethird link 90 is rotatably connected to the sample block assembly atpivot point 92. By revolution of the first end of the first link aboutthe central axis 76 of the motor, the first link causes the first end ofthe second link 84 to rotate partially about the stationary pivot point86, thus causing the third link to press upward against the sample blockassembly at pivot point 92. The positioning mechanism is connected tothe sample block assembly by, for example, a pin at pivot point 92. As aresult of this linkage arrangement, the positioning mechanism causes thesample block assembly to move vertically from the downward or “first”position shown in FIGS. 2A and 2B to the upward or “second” positionshown in FIG. 2C. It should be understood that the positioning mechanismof FIGS. 2A-2C is by way of example only.

[0045] As shown in FIG. 1, the positioning mechanism 70 may include twosets of links, one on each lateral side of the sample block assembly.The second set of links is a mirror image of the first set of links. InFIG. 1, the second set of links includes first link (not shown), secondlink 84′, and third link 90′. With a configuration having two sets oflinks, an individual motor may be utilized for each of the sets oflinks, or alternatively, a single motor may be utilized for both sets oflinks. In another variation, a single set of links may be used insteadof two sets of links. In a further variation, more than two sets oflinks may be used.

[0046] The positioning mechanism may also include at least one guidemember for guiding the sample block assembly in the vertical direction.The guide member can be configured to prevent the sample block assemblyfrom moving in the horizontal direction. Any known type of guide membermay be utilized. In the embodiment shown in FIGS. 1 and 2A-2C, the guidemember includes a plurality of vertical shafts 96 fixedly attached tothe lateral sides of the sample block assembly 50. As shown in FIG. 1,the vertical shafts are positioned on each lateral side of the samplewell tray holder 30 and sample well tray 14. Each vertical shaft 96 isreceived within bearing member 98. Bearing member is stationarilymounted adjacent the optical detection system. Each vertical shaft 96slides within a corresponding cylindrical opening in the bearing member98. The bearing members 98 and vertical shafts 96 may include any typeof known bearing arrangement.

[0047] Alternatively, in another variation, the vertical shaft could bestationarily fixed to the thermal cycling device so that the sampleblock assembly translates vertically relative to the vertical shaft.With such an arrangement, the bearing structures would be mounted withincylindrical openings in the sample block assembly for receiving thevertical shafts.

[0048] The guide member may be any other type of known guide membercapable of limiting movement of the sample block assembly in thehorizontal direction as the sample block assembly is moved in thevertical direction. For example, the guide member could include any typeof vertical guiding structure adjacent the sample block assembly. Itshould be understood that the guide member shown in FIGS. 2A-2C is byway of example only.

[0049] An operation of the thermal cycling device for the embodiment ofFIGS. 1 and 2A-2C is further described below. First, with the samplewell tray holder 30 in an outward position as shown in FIG. 2A, a samplewell tray 14 is placed in the sample well tray holder. The sample welltray can be dropped into the recess defined by downwardly projectingholder structure 38 shown in FIG. 5. The sample well tray 14 may beplaced in the sample well tray holder 30 either manually or robotically.

[0050] In FIG. 2A, the sample block assembly 50 is in a downward or“first” position so that a gap is created between the optical detectionsystem 12 and the uppermost surface of the sample block 58. The gap thatis created is larger than the vertical dimension of the sample well trayholder 30 and sample well tray 14.

[0051] After the sample well tray 14 is placed in the sample well trayholder 30, the sample well tray holder is horizontally translated intothe thermal cycling device 10 until the sample well tray reaches aposition where the sample wells of the sample well tray align with therecesses 52 of the sample block 58. The horizontal translation may becaused by an operator or a robot pressing on the sample well tray. Inthe embodiment shown in FIGS. 1 and 2A-2C, the sample well tray holder30 can be horizontally translated until each of the ninety-six samplewells align with a corresponding recess 52 in the sample block 58. FIG.2B shows the sample well tray holder 30 and sample well tray 14 in theposition where the sample wells 20 are aligned with correspondingrecesses in the sample block 58. As shown in FIG. 2B, the sample blockassembly 50 can remain in the downward position until the sample welltray is fully inserted into the thermal cycling device and aligned.

[0052] After the sample well tray 14 has been fully inserted into thethermal cycling device 10 and proper alignment has been achieved betweenthe sample wells 20 and the recesses 52 of the sample block (as shown inFIG. 2B), the motor 72 can be actuated to begin a revolution of thefirst end 80 of the first link 78. As the first end 80 of the first link78 begins to revolve around the central axis 76 of the motor, the pivotpoint 88 is moved leftward as shown in FIG. 2C, and the pivot point 92of the second end of the third link imparts an upward force on thesample block assembly 50. As a result, the sample block assembly 50 ismoved upward so that the top surface 54 of the sample block firmlycontacts the bottom surface of the sample well tray 14. In the upwardposition (also referred to as the “second position”) shown in FIG. 2C,the sample block assembly 50 is firmly positioned against the samplewell tray 14 so that the sample wells 22 are seated against the sampleblock. The thermal cycling device 10 is now ready for thermal cyclingprocesses.

[0053] At any desired time, e.g., after the thermal cycling processesare completed, the sample well tray 14 can be removed by actuating themotor so that the sample block assembly 50 moves to a downward position(as shown in FIG. 2B), and then horizontally translating the sample welltray holder 30 and sample well tray 14 to the position shown in FIG. 2A.The sample well tray 14 may then be removed from the sample well trayholder 30.

[0054] The amount of vertical displacement of the sample block assembly50 between the downward (“first”) and upward (“second”) positionsdepends on the specific application, the type and size of sample welltray that is utilized, and other practical concerns. For example, in anapplication for use with a 96-well sample well tray, the amount ofvertical displacement would typically be between about 0.5 to 1.5inches, but it could be much greater or much less. In an applicationwith a 384-well sample tray having smaller sample wells, or a microcard,the amount of vertical displacement of the sample block assembly may beless. For practical purposes however, it may also be desirable tovertically displace the sample block assembly a much greater distance inorder to provide better access to the inside of the device forinspection or maintenance.

[0055] In accordance with various embodiments, the optical detectionsystem 12 can be mounted in a substantially stationary manner in thethermal cycling device during insertion and removal of the sample welltray to and from the thermal cycling device, during thermal cycling, andduring all steps therebetween.

[0056] In accordance with further various embodiments of the positioningmechanism, the plurality of links comprises a first link and a secondlink. The first link has a first end rotatably connected to a stationarypivot point. The first link also has a second end comprising a handlefor manual manipulation of the first link. The second link has a firstend rotatably connected to a pivot point on the first link. The secondlink also has a second end rotatably connected to the sample blockassembly.

[0057] Further various embodiments of the sample block assemblypositioning mechanism contemplate structure such as shown in FIGS.3A-3C. The positioning mechanism is generally designated by thereference number 100 in FIGS. 3A-3C. The positioning mechanism includesa plurality of links such as first link 102 and second link 104. Asshown in FIG. 3A, the first link 102 has a first end rotatably connectedto a stationary pivot point 106 and a second end defining a handle 108for manual manipulation of the first link. In FIGS. 3A-3C, the firstlink 102 is in the shape of a connecting rod with a bend as shown inFIG. 3A. The handle 108 of the first link 102 defines a door 112corresponding to an opening 114 in the thermal cycling device. The door112 is configured to cover the opening 114 in the thermal cycling devicewhen the handle is actuated in a manner described below. Although thedoor is shown having an arcuate shape on the inner surface, any othersuitable shape is also acceptable.

[0058] As shown in FIG. 3A, the second link 104 has a first endrotatably connected to a pivot point 118 positioned on first link 102.The second link 104 has a second end rotatably connected to the sampleblock assembly 50 at pivot point 120. By the linkage arrangementdescribed above, the actuation of the handle 108 will cause the sampleblock assembly 50 to translate in the vertical direction.

[0059] An operation of the thermal cycling device for the embodiment ofFIGS. 3A-3C will be briefly described below. To the extent that thefollowing operation is similar to the operation described above for theembodiment shown in FIGS. 1 and 2A-2C, a detailed description of theoperation will not be repeated. Moreover, the same reference numberswill be used to refer to the same or like parts as shown in theembodiment of FIGS. 1 and 2A-2C. FIG. 3A shows the sample well trayholder 30 and sample well tray 14 in an outward position. In FIG. 3A,the sample block assembly 50 is in the downward or “first” position. Thesample well tray holder 30 is then inserted into the thermal cyclingdevice 10 by translating in the horizontal direction until the samplewell tray 14 reaches its proper aligned position (shown in FIG. 3B)between the optical detection system and the sample block assembly.

[0060] After the sample well tray 14 reaches its aligned position, anoperator may manually press against the handle 108 to rotate the firstlink 102 about the stationary pivot point 106. In another embodiment,the handle may be rotated robotically. In either case, the clockwiserotation (in reference to FIGS. 3A-3C) of the first link 102 results inthe pivot point 118 moving upward, thereby causing the pivot point 120on the second link 104 to move upward. The upward movement of the secondlink results in translation of the sample block assembly 50 in an upwardvertical direction to an upward or “second” position (shown in FIG. 3C).The positioning mechanism is configured so that the door 112 is fullyclosed as shown in FIG. 3C when the top surface of the sample blockfirmly contacts the sample well tray. When the sample block assembly isin the upward position, as shown in FIG. 3C, the thermal cycling deviceis ready for thermal cycling processes.

[0061] At any desired time, e.g., upon completion of the thermal cyclingprocesses, the handle 108 may be rotated counterclockwise, therebytranslating the sample block assembly 50 back to the downward positionshown in FIG. 3B. The sample well tray holder can then be slid from thethermal cycling device and returned to the position shown in FIG. 3A,and the sample well tray 14 may be removed from the sample well trayholder.

[0062] In accordance with still further embodiments of the positioningmechanism, the plurality of links can comprise a first link and a secondlink. The first link is rotatably connected to a stationary pivot point.The first link has a first end rotatably connected to the second linkand a second end comprising a handle for manual manipulation of thefirst link. The second link has a first end rotatably connected to thefirst end of the first link and a second end rotatably connected to thesample block assembly.

[0063] Such embodiments of the positioning mechanism include that shownin FIGS. 4A-4C. As shown in FIGS. 4A-4C, the positioning mechanism isgenerally designated by reference number 130. The positioning mechanism130 includes a plurality of links such as first link 132 and second link134. As shown in FIGS. 4A-4C, the first link 132 is rotatably connectedto a stationary pivot point 136. The first link 132 has a first endrotatably connected to the second link 134 at a pivot point 138. Thefirst link includes a second end comprising a handle 140 for manual orautomatic manipulation of the first link 132. The second link 134includes a first end rotatably connected to the first end of the firstlink at pivot point 138. The second link 134 further includes a secondend rotatably connected to the sample block assembly 50 at pivot point142.

[0064] As shown in FIGS. 4A-4C, the first link 132 includes a firstsegment 144 and a second segment 146. In FIGS. 4A-4C, the first segment144 and second segment 146 of the first link are substantiallyperpendicular to each other. This angle is by way of example only, asthe linkages may have various configurations. By the linkage arrangementdescribed above, the actuation of the handle 140 will cause the sampleblock assembly to translate in the vertical direction.

[0065] An operation of the thermal cycling device for the positioningmechanism of FIGS. 4A-4C will be briefly described below. To the extentthat the following operation is similar to the operation for the otherembodiments described above, a detailed description of the operationwill not be repeated. FIG. 4A shows the sample well tray holder 30 andsample well tray 14 in an outward position. In FIG. 4A, the sample blockassembly 50 is in the downward or “first” position. The sample well trayholder 30 is then inserted into the thermal cycling device 10 bytranslating in the horizontal direction until the sample well trayreaches its proper aligned position (shown in FIG. 4B).

[0066] After the sample well tray reaches its aligned position, anoperator may manually or automatically press downward against the handle140 to rotate the first link 132 about the stationary pivot point 136 ina counterclockwise direction (in reference to FIGS. 4A-4C). Thiscounterclockwise rotation of the first link 132 results in the pivotpoint 138 moving upwardly thereby causing the second link 134 to moveupwardly. The upward movement of the second link results in translationof the sample block assembly 50 in an upward vertical direction to anupward or “second” position. FIG. 4C shows the sample block assembly inthe upward or “second” position. When the sample block assembly is inthe upward position, as shown in FIG. 4C, the thermal cycling device isready for thermal cycling processes.

[0067] At any desired time, e.g., upon completion of the thermal cyclingprocesses, the handle 104 may be rotated clockwise, thereby translatingthe sample block assembly 50 back to the downward position as shown inFIG. 4B. The sample well tray holder 30 can then be slid from thethermal cycling device and returned to the position shown in FIG. 4A,and the sample well tray 14 may be removed from the sample well trayholder.

[0068] The sample block assembly positioning mechanisms shown in thefigures are provided for purposes of example only. Other positioningmechanisms could be, for example, a hydraulic, a spring, a lever, a cam,a solenoid, or any other suitable motion-producing device.

[0069] As is clear from the above description, the present inventionincludes a method of performing nucleic acid amplification on aplurality of biological samples positioned in a sample well tray in athermal cycling device. The method includes the step of placing thesample well tray into a sample well tray holder. The sample well tray 14shown in the figures is configured for placement into a correspondingrecess in the sample well tray holder 30.

[0070] The method further includes the step of translating the samplewell tray holder and sample well tray into the thermal cycling deviceuntil the sample well tray is aligned with a sample block assemblypositioned beneath the sample well tray. In one aspect, the translationof the sample well tray holder is in the horizontal direction. Thealigned position is shown for example in FIG. 2B. The method furtherincludes the step of translating the sample block assembly from a firstposition to a second position. In one aspect, the translation of thesample block assembly is in the vertical direction. In the firstposition, the sample block assembly permits the sample well tray totranslate into alignment with the sample block assembly. The firstposition of the sample block assembly 50 is shown for example in FIG.2B. In the second position, the sample block assembly is positionedvertically upward relative to the first position in order to contact thesample block assembly to the sample well tray. The second position ofthe sample block assembly 50 is shown for example in FIG. 2C.

[0071] The method further comprises thermally cycling the device whilesimultaneously optically detecting the samples. An optical detectionsystem 12 is positioned within the thermal cycling device 10 fordetecting the characteristics of the sample. The method furthercomprises translating the sample block assembly from the second positionto the first position. Finally, the method comprises the step ofremoving the sample well tray from the thermal cycling device. Theoptical detection system remains substantially stationary throughout theabove steps.

[0072] It is clear that the present invention is not limited to theexamples shown. For example, a thermal cycling device could beconfigured to handle several sample well trays, e.g., positioned side byside. Such an arrangement could include a corresponding optical systemand sample block.

[0073] It will be apparent to those skilled in the art that variousmodifications and variations can be made to the structure. Thus, itshould be understood that the invention is not limited to the examplesdiscussed in the specification. Rather, the present invention isintended to cover modifications and variations.

What is claimed is:
 1. A thermal cycling device, comprising: a sampleblock assembly; an optical detection system positioned above the sampleblock assembly; and a sample well tray holder including a tray-receivingregion configured to hold a sample well tray, the sample well trayholder configured to translate the sample well tray into alignment withthe sample block assembly, wherein the sample block assembly is adaptedfor movement between a first position permitting the translation of thesample well tray into alignment with the sample block assembly, and asecond position, upward relative to the first position, where the sampleblock assembly contacts the sample well tray.
 2. The thermal cyclingdevice of claim 1, wherein the optical detection system is adapted toremain substantially stationary during insertion and removal of thesample well tray from the thermal cycling device.
 3. The thermal cyclingdevice of claim 1, wherein the sample block assembly comprises a sampleblock for contacting the sample well tray when the sample block assemblyis in the second position.
 4. The thermal cycling device of claim 3,further comprising a positioning mechanism configured to translate thesample block between the first and second positions.
 5. The thermalcycling device of claim 4, wherein the positioning mechanism comprises aplurality of links.
 6. The thermal cycling device of claim 5, whereinthe positioning mechanism is configured so that movement of one of theplurality of links causes movement of another of the plurality of links,thereby causing the translation of the sample block assembly between thefirst and second positions.
 7. The thermal cycling device of claim 5,wherein the positioning mechanism further comprises a motor, and furtherwherein the plurality of links comprises a first link, a second link,and a third link, and further wherein a first end of the first link isrotatably connected to the motor, a second end of the first link isrotatably connected to the first end of both the second link and thethird link, the second link having a second end rotatably connected to astationary pivot point, the third link having a second end rotatablyconnected to the sample block assembly, and further wherein the motorcauses the first link to translate, thereby causing the second end ofthe third link to translate the sample block assembly between the firstand second positions.
 8. The thermal cycling device of claim 7, whereinthe plurality of links comprises a first set of links and a second setof links, the first and second set of links being positioned on oppositesides of the sample block assembly.
 9. The thermal cycling device ofclaim 5, wherein the plurality of links comprises a first link and asecond link, the first link having a first end rotatably connected to astationary pivot point, the first link having a second end comprising ahandle for manipulation of the first link, the second link having afirst end rotatably connected to a pivot point on the first link, thesecond link having a second end rotatably connected to the sample blockassembly, wherein the rotation of the first link about the stationarypivot point causes the second link to translate, thereby translating thesample block assembly between the first and second positions.
 10. Thethermal cycling device of claim 9, wherein the handle of the first linkfurther comprises a door corresponding to an opening in the thermalcycling device, wherein the door covers the opening in the thermalcycling device when the sample block assembly is in the second position.11. The thermal cycling device of claim 9, wherein the plurality oflinks comprises a first set of links and a second set of links, thefirst and second set of links being positioned on opposite sides of thesample block assembly.
 12. The thermal cycling device of claim 5,wherein the plurality of links comprises a first link and a second link,the first link being rotatably connected to a stationary pivot point,the first link having a first end rotatably connected to the secondlink, the first link having a second end comprising a handle for manualmanipulation of the first link, the second link having a first endrotatably connected to the first end of the first link, the second linkhaving a second end rotatably connected to the sample block assembly,wherein the rotation of the first link about the stationary pivot pointcauses the second link to translate, thereby translating the sampleblock assembly between the first and second positions.
 13. The thermalcycling device of claim 12, wherein the plurality of links comprises afirst set of links and a second set of links, the first and second setof links being positioned on opposite sides of the sample blockassembly.
 14. The thermal cycling device of claim 1, wherein the thermalcycling device is configured to perform thermal cycling when the samplewell tray is aligned with the sample block assembly and the sample blockassembly is positioned in the second position.
 15. The thermal cyclingdevice of claim 1, wherein the tray-receiving region of the sample welltray holder comprises a recess in which the sample well tray may bepositioned.
 16. The thermal cycling device of claim 1, wherein thethermal cycling device is a real-time PCR machine.
 17. A method ofperforming nucleic acid amplification on a plurality of biologicalsamples positioned in a sample well tray in a thermal cycling device,comprising the steps of: placing the sample well tray onto atray-receiving region of a sample well tray holder; translating thesample well tray holder and sample well tray into the thermal cyclingdevice until the sample well tray is aligned with a sample blockassembly positioned beneath the sample well tray; translating the sampleblock assembly from a first position wherein the sample block assemblypermits the sample well tray to translate into alignment with the sampleblock assembly, to a second position wherein the sample block assemblyis positioned vertically upward relative to the first position tocontact the sample well tray; thermally cycling the device whilesimultaneously optically detecting the samples; translating the sampleblock assembly from the second position to the first position; andremoving the sample well tray from the thermal cycling device, whereinthe optical detection system remains substantially stationary throughoutthe above steps.
 18. The method of performing nucleic acid amplificationof claim 17, wherein the steps of translating the sample block assemblyinclude the step of imparting a force on a first link in order to createmovement of the first link.
 19. The method of performing nucleic acidamplification of claim 18, wherein the movement of the first linkimparts a force on a second link to create movement of the second linkand the sample block assembly.
 20. A thermal cycling device, comprising:an optical detection system; a sample block adapted for movement along afirst path, toward and away from the optical detection system; and asample well tray holder including a tray-receiving region, the samplewell tray holder being adapted for movement along a second path, towardand away from a position whereat the tray-receiving region is disposedbetween the optical detection system and the sample block, wherein theoptical detection system is adapted to remain substantially stationaryduring movement of the sample block and the sample well tray holderalong the first and second paths.
 21. The thermal cycling device ofclaim 20, wherein the sample block is configured to allow the samplewell tray holder to move along the second path when the sample block isin a first position away from the optical detection system.
 22. Thethermal cycling device of claim 21, wherein the sample block isconfigured to contact a sample well tray received in the tray-receivingregion of the sample well tray holder when the tray-receiving region isdisposed between the optical detection system and the sample block, andthe sample block is in a second position toward the optical detectionsystem.
 23. The thermal cycling device of claim 22, further comprising apositioning mechanism configured to translate the sample block betweenthe first and second positions.
 24. The thermal cycling device of claim23, wherein the positioning mechanism comprises a plurality of links.25. The thermal cycling device of claim 24, wherein the positioningmechanism is configured so that movement of one of the plurality oflinks causes movement of another of the plurality of links, therebycausing the translation of the sample block between the first and secondpositions.
 26. The thermal cycling device of claim 24, wherein thepositioning mechanism further comprises a motor, and further wherein theplurality of links comprises a first link, a second link, and a thirdlink, and further wherein a first end of the first link is rotatablyconnected to the motor, a second end of the first link is rotatablyconnected to the first end of both the second link and the third link,the second link having a second end rotatably connected to a stationarypivot point, the third link having a second end rotatably connected tothe sample block, and further wherein the motor causes the first link totranslate, thereby causing the second end of the third link to translatethe sample block between the first and second positions.
 27. The thermalcycling device of claim 26, wherein the plurality of links comprises afirst set of links and a second set of links, the first and second setof links being positioned on opposite sides of the sample block.
 28. Thethermal cycling device of claim 24, wherein the plurality of linkscomprises a first link and a second link, the first link having a firstend rotatably connected to a stationary pivot point, the first linkhaving a second end comprising a handle for manipulation of the firstlink, the second link having a first end rotatably connected to a pivotpoint on the first link, the second link having a second end rotatablyconnected to the sample block, wherein the rotation of the first linkabout the stationary pivot point causes the second link to translate,thereby translating the sample block between the first and secondpositions.
 29. The thermal cycling device of claim 28, wherein thehandle of the first link further comprises a door corresponding to anopening in the thermal cycling device, wherein the door covers theopening in the thermal cycling device when the sample block is in thesecond position.
 30. The thermal cycling device of claim 28, wherein theplurality of links comprises a first set of links and a second set oflinks, the first and second set of links being positioned on oppositesides of the sample block.
 31. The thermal cycling device of claim 24,wherein the plurality of links comprises a first link and a second link,the first link being rotatably connected to a stationary pivot point,the first link having a first end rotatably connected to the secondlink, the first link having a second end comprising a handle for manualmanipulation of the first link, the second link having a first endrotatably connected to the first end of the first link, the second linkhaving a second end rotatably connected to the sample block, wherein therotation of the first link about the stationary pivot point causes thesecond link to translate, thereby translating the sample block betweenthe first and second positions.
 32. The thermal cycling device of claim31, wherein the plurality of links comprises a first set of links and asecond set of links, the first and second set of links being positionedon opposite sides of the sample block.
 33. The thermal cycling device ofclaim 20, wherein the thermal cycling device is configured to performthermal cycling when the tray-receiving region of the sample well trayholder is disposed between the optical detection system and the sampleblock, and the sample block is in a position toward the opticaldetection system.
 34. The thermal cycling device of claim 20, whereinthe tray-receiving region of the sample well tray holder comprises arecess in which a sample well tray may be positioned.
 35. The thermalcycling device of claim 20, wherein the thermal cycling device is areal-time PCR machine.